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Other things to consider, the torsional damper from a 6.2 will not work on the optimizer.
The water pump backing plates varies depending on which water pump you end up running.
You need to get one with cylinder heads that match your intake configuration. Angled vs straight holes. You'll need...
In addition to the bellhousing and motor mount bolts, the oil cooler lines are 1/2 NPT on the Optimizer. You'll need to bush down to 3/8 if you want to reuse your 6.2 fittings.
If the bigger unit is available I see no reason not to run it. We run our generators at 10% load for 99% of their run time and they do fine. The big 8.1L engines got to burning oil but made it to 35k hours run-time. We replaced with 4.5 liter engines. Fuel consumption doesn't change much, they...
Here is a description of various connection diagrams for the generator.
https://www.marathongenerators.com/generators/docs/manuals/Connection%20Diagrams.pdf
From your picture, I don't think that is enough bubbles to indicate a misfire causing head gasket leak.
Crack injector lines to see if you can pinpoint the misfiring cylinder. There will be no change in idle when you hit the bad one.
Do you have an acetylene torch? Once the cage is off turn the spindle upside-down and heat the inner race a rapidly as you can. It will fall right off.
A bit late but I must add a correction about surge and stall. They are too separate conditions.
Surge is a lack of flow through the compressor wheel. The compressor needs flow to create a load and keep it from overspending. A clogged air filter can cause surge.
Stall is a lack of flow through...
If you put a 2:1 gearbox between the 6.0 engine and transmission you will likely exceed the torque rating of the transmission. 2 x 380ftlb = 760 which is greater than 425 ftlb.
Torque at the crankshaft is unimportant, it's horsepower to the wheels that matters. If you change the gearing to work with the 6.0 it will outperform the 6602. Of you change the gearing to work with the 6.0 it will likely not work with your budget.
At idle it can take engines quite a while to come up to temp. This isn't ideal. It can also be caused by bad thermostats.
Since the water in the oil isn't back it's probably ingestion through the intake or exhaust.